The holes or the "eyes" are made by the carbon dioxide bubbling up. The carbon dioxide is the waste eliminated by the bacteria, Streptococcus salivarius subspecies thermophilus, Lactobacillus (Lactobacillus helveticus or Lactobacillus delbrueckii subspecies bulgaricus), and Propionibacterium (Propionibacterium freudenreichii subspecies shermanii).

How the holes are made